Metadata-Version: 1.2
Name: MDCatch
Version: 0.9.3
Summary: Fetch metadata from EPU / SerialEM and launch on-the-fly pre-processing
Home-page: https://github.com/azazellochg/MDCatch
Author: Grigory Sharov
Author-email: gsharov@mrc-lmb.cam.ac.uk
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/azazellochg/MDCatch/issues
Project-URL: Source, https://github.com/azazellochg/MDCatch
Description: # MDCatch
        ## Still in development, but you are welcome to try!
        A simple PyQt5 app to fetch metadata from EPU or SerialEM.
        It parses the first found EPU xml and SerialEM mdoc file associated with a data collection session. In case of SerialEM you need to enable saving mdoc file for each movie.
        
        ### Prerequisites / installation:
          - Python 3 and PyQt5. If you don't have PyQt5 module in your system python3 then create a virtual environment:
            ```
            python3 -m venv venv
            source venv/bin/activate
            pip install PyQt5
            ```
          - Relion 3.1 or Scipion 3.0 sourced in your `PATH` (at the moment Scipion 3 is not ready!)
          - Preprocessing templates: `Schedules` folder for Relion, `template.json` for Scipion
          - Edit `config.py` to adjust it to your settings
         
        ### Running
         Simply `python3 run.py`. User only needs to provide: 
          - path to EPU session folder or path to folder with SerialEM movies/mdoc files
          - particle size (A)
          - username
        
        ### Working principle
        The idea is to launch the app on a separate OTF machine as soon as EPU/SerialEM starts data collection and the first movie is acquired.
        
          1. check if username exists in the NIS database (`ypmatch username passwd`)
          2. find and parse the first xml/mdoc file, getting all acquisition metadata
          3. create a Relion/Scipion project folder `username_microscope_date_time` inside PROJECT_PATH (or inside Scipion default projects folder)
          4. create symlinks for movies, gain reference, defects file, MTF in the project folder
          5. modify existing Relion Schedules/Scipion templates then launch Relion/Scipion on-the-fly processing
        
        ### Screenshots
        
        ![Screenshot_20200103_182047](https://user-images.githubusercontent.com/6952870/71741099-e2c6d200-2e55-11ea-9c98-66a14dc8cb2e.png)
        ![Screenshot_20200103_182116](https://user-images.githubusercontent.com/6952870/71741103-e5292c00-2e55-11ea-95c3-4cf51de7382c.png)
        
        ### TODO
          - beam tilt is parsed but not used since we parse only a single xml/mdoc for the whole session
          - SerialEM conversions: gain ref dm4->mrc, defects SerialEM->Relion
          - K3 EPU 2.6.1 gain file is a rubbish tif, to be fixed by TFS
          - use GAIN_DICT from config
        
Keywords: cryo-em python qt5 epu serialem
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
